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Genomes are More than Just Genes
Searching for and describing transposable elements
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Peter Arensberger
California State Polytechnic University, Pomona
Château du Clos Lucé
Invaders
Rotavirus
Plasmodium vivax
Salmonella typhimurium
Herves (Transposon)
>gi|42600942|gb|AY462096.1| Anopheles gambiae PEST transposon Herves,
complete sequence
TAGAGTTGTGCCTCAAGAACCAGAACTGTACGATTCATTCAATTCATCCTAAAGAACGAACGACCTACGT
TCATCTAATCAACGTTCATCGATTCTTTATAAATTATAATGTGTTGAGTTGTTCATGAAAATAACCCGGG
TAGGAACCCGTCGAAATGAAGAACGTCCTAGTACGCCAGGTCGTTCATTCCCCCCATACAAATATGAACG
TGAATCGTATGACCAGGACGTTCACGAAAAGAACGTCATACCCGTCGAAATAAAGAACGTCCTAGCAAGC
CAGGTCGTTCATTCCCCCCATTCAAAATGAACGTGAATCGTATGACCAGGACGTTCACGAAAAGAACGTC
CTACCCGTCGAAATAAAGAACGTCCTAGCAAGTCAGGTCGTTCATTTTTTCCCATACAAATATGAACGTG
(...)
Discovery of Transposable
Elements
Changed the traditional view of genetics
Late 1940's reported on the discovery of two loci
Activator (Ac) and Dissociation (Ds)
Activator-Dissociation system
Dissociation (Ds) → A genetic region
that PREVENTS expression of color
Activator (Ac) → A genetic region
that is able to move the Ds region
around
purple color is made
no color
no color
purple color is made
A more Broad Definition of
Transposable Elements
Genomic sequences that encode the protein or proteins necessary to
for their movement within the genome
Many, categories of transposable elements, including
DNA transposons
LINEs
SINEs
LTR retrotransposons
...
Human Genome Landscape
Approximately half the human
genome is composed
of sequences derived from
transposable element
sequences
Human Genome Landscape
Approximately half the human
genome is composed
of sequences derived from
transposable element
sequences
Transposable element
Transposable Elements Derived
Sequences are Abundant in
Most Eukaryotic Genomes
Organism
Percent of genome derived from transposable
element sequences
Human
45%
Opossum
55%
Malaria mosquito
47%
Corn (Maize)
85%
Why are “we” at War with
Transposable Elements?
Transposable element movement is generally deleterious
Movement is particularly dangerous into germline cells
From Morell et al. (2002, doi 10.1105/tpc.010358), effect of knocking out a
gene involved in transposable element regulation
What Can we Do Against
Transposable Elements?
●
●
●
Excise them from the genome
Prevent their associated proteins from being produced
• histone acetylation
• methylation
• small RNA interference
Sexual reproduction has been suggested to play a role in reducing
the number of deleterious transposable elements
The computing Honey Pot
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The computing Honey Pot
Transposable element
g
nua
e
regular genome
sequences
master regulatory
loci
What Makes a Successful
Transposable Element?
High copy number may actually be detrimental for a
transposable element
Fig. 10b from
Chinwalla, Asif T., et al.
(2002 doi:10.1038/nature01262)
Are Transposable Elements All Bad?
Our RAG1 gene is probably
derived from a transposable
element
Transposable element sequences
can affect gene expression,
enhancing expression in some
cases
cooked rat
Transposable element sequences can be harnessed for
research purposes
How does all this relate to France?
Two main lines of research
1) Updating the most fundamental levels of transposable element
classification
2) Developing a methodology for transposable element annotation
in unassembled genomes, with applications in bird genomes
Transposable Element Classification
Transposable elements are a very diverse group
Current eukaryotic transposable element classification
schemes divide these sequences by their use or not of
an RNA intermediate.
Transposable element history may not follow that of the
host.
Very different elements may recombine to form a new
element type
The Problem with Keeping the
Current Classification
Current classification is fundamentally anchored in
a division that is not biologically based.
This division artificially partitions the scientific community
This situation leads to erroneous conclusions based on
implied phylogeny
Classification of viruses may offer a path forward to
rectify this situation in transposable elements
So we wrote a paper...
A survey of transposable element classification systems – a call for a
fundamental update to meet the challenge of their diversity and complexity
Benoît Piégu1, Solenne Bire1,2, Peter Arensburger1,3,* & Yves Bigot1,*
...and got slammed!
Identifying the repeated portion of
an unassembled genome
C value
Struthio camelus
2.16
Gallus gallus
1.25
Archilochus alexandri
0.91
Haliaeetus vocifer
1.43
C
% TE
0.27
12%
Culex quinquefaciatus
0.54 – 1.02
29%
Aedes aegypti
0.81 - 1.25
42%
Anopheles gambiae
What are the differences in genome
size due to?
● Transposable elements
● Satellite sequences
● Other sequences
RepeatExplorer
Jiri Macas
Pavel Neuman
Petr Novak
RepeatExplorer
How it works (briefly)
GCTCTTCCGATCTGGCTAAG
|||||||||| |||
CCGATCTGGCAAAGTACGG
RepeatExplorer
GCTCTTCCGATCTGGCTAAG
CCGATCTGGCTAAGGCCGATTT
GGCCGATTTACTGGGCG
TTTACTGGGCGTTTCT
GATCGATCGATCGATCGATC
GATCGATCGATCGATCTTCC
GATCGATCGATCGATCGATCCAG
ATCGATCGATCGATCGATC
Conclusions of RepeatExplorer
analysis of bird genomes
Found little differences in transposable element or
in satellite sequences between bird species